Genome Structure, Evolution, and Host Shift of Nosema

<i>Nosema</i> is a diverse fungal genus of unicellular, obligate symbionts infecting various arthropods. We performed comparative genomic analyses of seven <i>Nosema</i> species that infect bees, wasps, moths, butterflies, and amphipods. As intracellular parasites, these species exhibit significant genome reduction, retaining only about half of the genes found in free-living yeast genomes. Notably, genes related to oxidative phosphorylation are entirely absent (<i>p</i> < 0.001), and those associated with endocytosis are significantly diminished compared to other pathways (<i>p</i> < 0.05). All seven <i>Nosema</i> genomes display significantly lower G-C content compared to their microsporidian outgroup. Species-specific 5~12 bp motifs were identified immediately upstream of start codons for coding genes in all species (<i>p</i> ≤ 1.6 × 10^-72). Our RNA-seq data from <i>Nosema muscidifuracis</i> showed that this motif is enriched in highly expressed genes but depleted in lowly expressed ones (<i>p</i> < 0.05), suggesting it functions as a <i>cis</i>-regulatory element in gene expression. We also discovered diverse telomeric repeats within the genus. Phylogenomic analyses revealed two major <i>Nosema</i> clades and incongruency between the <i>Nosema</i> species tree and their hosts' phylogeny, indicating potential host switch events (100% bootstrap values). This study advances the understanding of genomic architecture, gene regulation, and evolution of <i>Nosema</i>, offering valuable insights for developing strategies to control these microbial pathogens.